# Show & Tell **URL:** https://community.brain-map.org/c/show-tell/7.md?page=1 [Latest](https://community.brain-map.org/latest.md) · [Categories](https://community.brain-map.org/categories.md) · [Tags](https://community.brain-map.org/tags.md) **Page:** 2 --- ## [Join us for Showcase Symposium 2020!](https://community.brain-map.org/t/join-us-for-showcase-symposium-2020/817)
**Author:** [@kaitlync](https://community.brain-map.org/u/kaitlync)\ **Replies:** 0\ **Last updated:** [December 10, 2020, 6:02pm UTC](https://community.brain-map.org/t/join-us-for-showcase-symposium-2020/817 "2020-12-10T18:02:00Z")
We are hosting our annual Showcase Symposium virtually next week, December 14-16. Hear recent research highlights from the Allen Institute for Brain Science and our Next Generation Leaders council members. Speakers will … --- ## [Open for (neuro)science tutorials: Introduction to the Allen Brain Map](https://community.brain-map.org/t/open-for-neuro-science-tutorials-introduction-to-the-allen-brain-map/816)
**Author:** [@kaitlync](https://community.brain-map.org/u/kaitlync)\ **Replies:** 0\ **Last updated:** [December 10, 2020, 5:51pm UTC](https://community.brain-map.org/t/open-for-neuro-science-tutorials-introduction-to-the-allen-brain-map/816 "2020-12-10T17:51:30Z")
Thanks for attending the webinar or viewing the video of the Open for (neuro)science: Introduction to the Allen Brain Map! This webinar provided an overview of the resources available through the Allen Brain Map, why the… --- ## [Displaying data in common coordinate framework - CCF reference space](https://community.brain-map.org/t/displaying-data-in-common-coordinate-framework-ccf-reference-space/781)
**Author:** [@Momo](https://community.brain-map.org/u/Momo)\ **Replies:** 6\ **Last updated:** [December 2, 2020, 8:47pm UTC](https://community.brain-map.org/t/displaying-data-in-common-coordinate-framework-ccf-reference-space/781 "2020-12-02T20:47:19Z")
Hi, I would like to ask how I can display some MRI and morphological data that I have brought to Common Coordinate Framework with Allen Brain tools. (Like making some heat maps in different mouse brain regions). Your h… --- ## [The Virtual Science Lab - Defining Cell Types by their Electrophysiology Q&A](https://community.brain-map.org/t/the-virtual-science-lab-defining-cell-types-by-their-electrophysiology-q-a/782)
**Author:** [@kaitlync](https://community.brain-map.org/u/kaitlync)\ **Replies:** 1\ **Last updated:** [November 13, 2020, 12:14am UTC](https://community.brain-map.org/t/the-virtual-science-lab-defining-cell-types-by-their-electrophysiology-q-a/782 "2020-11-13T00:14:38Z")
Thanks for attending the webinar or viewing the video of “The Virtual Lab: Defining Cell Types by their Electrophysiology” with @ajuavinett and @tmchartrand! This webinar demonstrated a lesson plan for college neuroscien… --- ## [Which database to use for thesis?](https://community.brain-map.org/t/which-database-to-use-for-thesis/702)
**Author:** [@smokey](https://community.brain-map.org/u/smokey)\ **Replies:** 1\ **Last updated:** [September 23, 2020, 3:11pm UTC](https://community.brain-map.org/t/which-database-to-use-for-thesis/702 "2020-09-23T15:11:01Z")
Dear people, I am currently writing my doctoral thesis. Since I have collected quite a lot of data for my empirical part, which I can’t simply write together in an Excel document, I thought about putting my data for the… --- ## [Standard method for creating dendrograms from neuron morphology data?](https://community.brain-map.org/t/standard-method-for-creating-dendrograms-from-neuron-morphology-data/690)
**Author:** [@Pathfinder\_Tenso](https://community.brain-map.org/u/Pathfinder_Tenso)\ **Replies:** 4\ **Last updated:** [September 15, 2020, 12:49am UTC](https://community.brain-map.org/t/standard-method-for-creating-dendrograms-from-neuron-morphology-data/690 "2020-09-15T00:49:20Z")
I have been working to create some dendrograms from existing neuron morphology data we have in a TrakEM2 project (FIJI plugin). I have converted the .xml project data into the SWC format which seems to be a good starting… --- ## [CCF rego 2020 competition](https://community.brain-map.org/t/ccf-rego-2020-competition/315)
**Author:** [@rusty](https://community.brain-map.org/u/rusty)\ **Replies:** 1\ **Last updated:** [August 26, 2020, 10:55pm UTC](https://community.brain-map.org/t/ccf-rego-2020-competition/315 "2020-08-26T22:55:41Z")
CCF Registration Competition Announcing the first Allen Institute for Brain Science CCF registration competition! A brief description of the competition motivation, format, and next steps is below. Motivation The Alle… --- ## [Using the brain observatory in the classroom](https://community.brain-map.org/t/using-the-brain-observatory-in-the-classroom/63)
**Author:** [@Eric](https://community.brain-map.org/u/Eric)\ **Replies:** 14\ **Last updated:** [May 7, 2020, 5:40pm UTC](https://community.brain-map.org/t/using-the-brain-observatory-in-the-classroom/63 "2020-05-07T17:40:52Z")
Hello everyone! Here at the UW we’ve been using the Brain Observatory in our computational neuroscience courses – as a final workshop / lecture and transition to (somewhat amazingly, I always think) actual open question… --- ## [Developing a brain atlas through deep learning](https://community.brain-map.org/t/developing-a-brain-atlas-through-deep-learning/458)
**Author:** [@asim](https://community.brain-map.org/u/asim)\ **Replies:** 1\ **Last updated:** [February 28, 2020, 10:32pm UTC](https://community.brain-map.org/t/developing-a-brain-atlas-through-deep-learning/458 "2020-02-28T22:32:05Z")
Hey everyone, Just wanted to share (SeBRe-Segmenting Brain Regions) a tool that I have developed recently to register an atlas/segment brain regions in analysing large scale mouse/human brain images. All the testing is … --- ## [Online bioinformatics masters?](https://community.brain-map.org/t/online-bioinformatics-masters/429)
**Author:** [@davidbrok5](https://community.brain-map.org/u/davidbrok5)\ **Replies:** 0\ **Last updated:** [February 3, 2020, 3:52pm UTC](https://community.brain-map.org/t/online-bioinformatics-masters/429 "2020-02-03T15:52:41Z")
Hi everyone, I’m a 25 year old project coordinator and RA at a biotech company and recently got a full-time conversion that includes tuition assistance. My background is biochemistry and molecular biology and I’m thinki… --- ## [CHAMBER expansion – which proteins would you be interested to see the distributions of?](https://community.brain-map.org/t/chamber-expansion-which-proteins-would-you-be-interested-to-see-the-distributions-of/402)
**Author:** [@kouichi\_c\_nakamura](https://community.brain-map.org/u/kouichi_c_nakamura)\ **Replies:** 0\ **Last updated:** [January 8, 2020, 2:08pm UTC](https://community.brain-map.org/t/chamber-expansion-which-proteins-would-you-be-interested-to-see-the-distributions-of/402 "2020-01-08T14:08:44Z")
CHAMBER (CHemoarchitectonic Atlas of the Mammalian Brain as an E-Resource) is an open resource for “chemoarchtectonics” of the brain, powered by OMERO, an open-source server software for image sharing, and hosted by MRC … --- ## [Histology & Immunohistochemistry: Compendium data available for analyzing the cytoarchitecture of the brain](https://community.brain-map.org/t/histology-immunohistochemistry-compendium-data-available-for-analyzing-the-cytoarchitecture-of-the-brain/369)
**Author:** [@brain](https://community.brain-map.org/u/brain)\ **Replies:** 1\ **Last updated:** [December 4, 2019, 12:34pm UTC](https://community.brain-map.org/t/histology-immunohistochemistry-compendium-data-available-for-analyzing-the-cytoarchitecture-of-the-brain/369 "2019-12-04T12:34:28Z")
The Allen Brain Map includes comprehensive data related to gene expression and anatomy across the mammalian brain. Accompanying the quantitative data for tissue- and cell-specific gene expression by mRNA detection, qual… --- ## [BrainModules an interactive viewing tool](https://community.brain-map.org/t/brainmodules-an-interactive-viewing-tool/365)
**Author:** [@riichirohira](https://community.brain-map.org/u/riichirohira)\ **Replies:** 0\ **Last updated:** [November 23, 2019, 12:26pm UTC](https://community.brain-map.org/t/brainmodules-an-interactive-viewing-tool/365 "2019-11-23T12:26:32Z")
We have made an interactive viewing tool using the Allen database. https://web.ece.ucsb.edu/~riichirohira/TopBM-2.06/index.html Spencer Smith introduced this tool on twitter: We thank people who made the Allen Mous… --- ## [Mouse neurons reconstruction -\> CCF alignment](https://community.brain-map.org/t/mouse-neurons-reconstruction-ccf-alignment/323)
**Author:** [@FedeClaudi](https://community.brain-map.org/u/FedeClaudi)\ **Replies:** 2\ **Last updated:** [October 31, 2019, 10:45pm UTC](https://community.brain-map.org/t/mouse-neurons-reconstruction-ccf-alignment/323 "2019-10-31T22:45:39Z")
Hi, I’m working on BrainRender, a python package to render mouse anatomical and morphological data (largely based on the Allen datasets). I’ve added the possibility to render cell morphologies from theCellTypesCache,… --- ## [Matlab tool to visualize input output strength of specific brain area](https://community.brain-map.org/t/matlab-tool-to-visualize-input-output-strength-of-specific-brain-area/257)
**Author:** [@robertooooo](https://community.brain-map.org/u/robertooooo)\ **Replies:** 1\ **Last updated:** [September 5, 2019, 2:51pm UTC](https://community.brain-map.org/t/matlab-tool-to-visualize-input-output-strength-of-specific-brain-area/257 "2019-09-05T14:51:40Z")
Hi, I want to share a tool I recently wrote to visualize input and output of a brain area of interest in Matlab. https://github.com/Robertooooooo/BRIO . Happy to receive feedback! Cheers --- ## [Our code for predicting cell type of neurons from Allen Cell DB](https://community.brain-map.org/t/our-code-for-predicting-cell-type-of-neurons-from-allen-cell-db/248)
**Author:** [@spookey](https://community.brain-map.org/u/spookey)\ **Replies:** 0\ **Last updated:** [August 23, 2019, 3:49am UTC](https://community.brain-map.org/t/our-code-for-predicting-cell-type-of-neurons-from-allen-cell-db/248 "2019-08-23T03:49:46Z")
Hi. It’s first post! I just wanted to share our work at GitHub. We used three kinds of machine learning methods(LASSO, random forest, ANN) for predicting transgenic cell marker. Electrophysiological features from Alle… --- ## [Mice, and more mice!](https://community.brain-map.org/t/mice-and-more-mice/196)
**Author:** [@amyb](https://community.brain-map.org/u/amyb)\ **Replies:** 0\ **Last updated:** [June 13, 2019, 10:22pm UTC](https://community.brain-map.org/t/mice-and-more-mice/196 "2019-06-13T22:22:15Z")
The Allen Institute works with the mouse as a model for brain research, to gain insight into the molecular and structural underpinnings of cell-level function. Many people are aware that the classic Allen Mouse Brain At… --- ## [Are there any publications using the Brain Observatory?](https://community.brain-map.org/t/are-there-any-publications-using-the-brain-observatory/24)
**Author:** [@saskiad](https://community.brain-map.org/u/saskiad)\ **Replies:** 3\ **Last updated:** [March 11, 2019, 9:14pm UTC](https://community.brain-map.org/t/are-there-any-publications-using-the-brain-observatory/24 "2019-03-11T21:14:04Z")
Tracking the same neurons across multiple days in Ca2+ imaging data. Sheintuch et al. https://www.sciencedirect.com/science/article/pii/S2211124717314304 SCALPEL: Extracting neurons from calcium imaging data. Peters… --- ## [Using the the mouse brain reference atlas for cell quantification: example publication](https://community.brain-map.org/t/using-the-the-mouse-brain-reference-atlas-for-cell-quantification-example-publication/115)
**Author:** [@brain](https://community.brain-map.org/u/brain)\ **Replies:** 0\ **Last updated:** [February 26, 2019, 8:01pm UTC](https://community.brain-map.org/t/using-the-the-mouse-brain-reference-atlas-for-cell-quantification-example-publication/115 "2019-02-26T20:01:39Z")
A really nice extension of the Allen Mouse Brain reference atlas has been published, for mapping single cell-level data. A Cell Atlas for the Mouse Brain by Ero et al (2018) maps presumptive cells from histological data … --- ## [RasterMap released as Python package](https://community.brain-map.org/t/rastermap-released-as-python-package/44)
**Author:** [@justin](https://community.brain-map.org/u/justin)\ **Replies:** 0\ **Last updated:** [September 7, 2018, 9:59pm UTC](https://community.brain-map.org/t/rastermap-released-as-python-package/44 "2018-09-07T21:59:38Z")
Carsen Stringer has released the amazing RasterMap in Python!! This amazing visualization technique clusters timeseries (spikes or calcium signals) & ranks them by similarity… an awesome way to visualize high-dimensio… --- ## [Some background into the Brain Observatory project](https://community.brain-map.org/t/some-background-into-the-brain-observatory-project/76)
**Author:** [@amyb](https://community.brain-map.org/u/amyb)\ **Replies:** 0\ **Last updated:** [November 19, 2018, 10:44pm UTC](https://community.brain-map.org/t/some-background-into-the-brain-observatory-project/76 "2018-11-19T22:44:10Z")
Here’s a fun YouTube video of the Brain Observatory in action, from the summer of 2018. Enjoy! --- ## [Cheat sheet for using the Brain Observatory](https://community.brain-map.org/t/cheat-sheet-for-using-the-brain-observatory/74)
**Author:** [@saskiad](https://community.brain-map.org/u/saskiad)\ **Replies:** 0\ **Last updated:** [November 19, 2018, 6:35pm UTC](https://community.brain-map.org/t/cheat-sheet-for-using-the-brain-observatory/74 "2018-11-19T18:35:23Z")
We made a two page cheat sheet, describing the dataset as well as some of the key functions of the SDK, that can be helpful for people getting started using this dataset. You can find it here --- ## [Allen Brain Observatory at Cosyne 19](https://community.brain-map.org/t/allen-brain-observatory-at-cosyne-19/77)
**Author:** [@amyb](https://community.brain-map.org/u/amyb)\ **Replies:** 0\ **Last updated:** [November 19, 2018, 11:05pm UTC](https://community.brain-map.org/t/allen-brain-observatory-at-cosyne-19/77 "2018-11-19T23:05:31Z")
Mark your calendars for the Allen Brain Observatory making an appearance at Cosyne 19, on Feb 28 2019. Looking forward to the tutorial! --- ## [Our code for population decoding is on github](https://community.brain-map.org/t/our-code-for-population-decoding-is-on-github/53)
**Author:** [@memming](https://community.brain-map.org/u/memming)\ **Replies:** 1\ **Last updated:** [September 17, 2018, 4:00pm UTC](https://community.brain-map.org/t/our-code-for-population-decoding-is-on-github/53 "2018-09-17T16:00:47Z")
First! Just wanted to point to our python notebook: https://github.com/catniplab/aboDecoding We used linear decoding methods for different subpopulations and extrapolated the results for a fair comparison across areas/… [Previous page](https://community.brain-map.org/c/show-tell/7.md)